The morning after their first bedroom romp (see “Double Agent”), Vaughn asks Sydney why she never calls him Michael. She tells him that she’s supposed to be graduating from grad school today. She says that she’s been thinking about why she didn’t drop out of school and resign herself to being an agent forever. “You’re going to quit the CIA, aren’t you?” Vaughn asks. Kendall, however, tells Sydney that he won’t let her resign. He says that they have a lot to clean up now that the Alliance has been destroyed (see “Phase One”), and Sloane is still an issue. Sydney replies that she did everything she told the CIA she would do, and now she wants out. Jack tells her that he’s always wanted her to have a normal life, but she is valuable to the CIA, so she should give the decision more thought. Sydney exclaims that she’s done letting other people control her life and doesn’t need anyone’s approval to quit. Kendall informs her that if she leaves the CIA, she won’t be able to talk to Irina anymore. Sydney visits Irina, who congratulates her on helping take down the Alliance. Sydney shares that she’s thinking of leaving the agency, which would mean giving up access to Irina. Her mother says that Sydney doesn’t owe her anything and shouldn’t base her decision on her. She adds that if Sydney decides to stay, she won’t see her anymore.

A couple named Neil (Christian Slater) and Elsa Caplan (Tracy Middendorf) take their son Aaron to an aquarium for his birthday, though Elsa notes that Caplan is distracted by something he’s been working on. They realize that Aaron is missing, and while they’re looking for him, Sark appears and tells Caplan that he can help find his son and his now-missing wife. At home, Sydney gets ready for graduation and seems to notice Allison acting strangely. Sloane calls to congratulate Sydney, noting that it’s there first completely honest conversation and she has nothing to say. Sydney blasts him and reveals that she’s fantasized about killing him many times. He tells her that he provided the intel the CIA used to take down the Alliance. He adds that as tempted as she probably is to hunt him down, she shouldn’t because they set each other free. Also, he’ll kill her if she tries. At the CIA, Sydney fills the others in on the call and learns that Caplan, a mathematician, was taken away by Sark after his family was kidnapped. Caplan studies how geometric objects fit together, so Sark may be using him to assemble a Rambaldi device that’s probably also a weapon. Sydney realizes that things like this will never stop happening. Kendall tells her that now is the time if she’s going to choose to resign. Sloane meets with Caplan and tells him that he’s going to help assemble a bunch of Rambaldi artifacts.

At the CIA, Sydney tells Dixon that he’s been cleared of knowing that anything bad was going on with SD-6. She adds that his friendship was the only thing that kept her sane while she was working as a double agent. He asks her how long she knew the truth about SD-6 and is furious that she lied to her own partner. At the ops center, however, Marshall is quickly adjusting to his new job. Dixon goes home and tells Diane that he doesn’t work at a bank. Marshall tells Sydney, Vaughn, and Jack that Sloane has been in contact with a cybernetic specialist named Holden Gendler. Jack goes out to see him, but he’s the guy Sloane killed in “Getaway.” Something in his eye socket is beeping and flashing. Back at the ops center, Marshall tells everyone that the device is an intra-ocular retinal implant Gendler used in self-experiments. Jack figures out that Sloane got Gendler to deactivate the device the Alliance put into him. Marshall uploads footage of the last thing Gendler saw, which was Sloane shooting him. They figure out that Sloane chartered a plane out of the Mojave Desert and decide to go get the flight data recorder to find out where he went. Sark tells a captive Elsa and Aaron that Caplan is helping him out with something, asking Elsa to make a recording for Caplan to tell him that Aaron will be harmed if he doesn’t cooperate.

In the Mojave, Vaughn poses as an arms dealer but has his expertise questioned. He proves himself and meets up with Sydney, who finds the data recorder. She gets caught, of course, and has to fight her way to safety. Diane comes home after a night at her sister’s and tells Dixon that she can’t know for sure if anything he’s ever said to her was true. He promises her that his love for her and their kids is true and he’ll never lie to her again. He adds that the CIA has offered him a job, but Diane says that she didn’t choose this kind of life, so if he wants the job, he’s on his own. Caplan tells Sloane that he’ll only help him if his family is released. Sloane plays a recording of Elsa begging Caplan to cooperate so Aaron won’t be harmed. Caplan needs a device he’s been developing in order to put the artifacts together; Sloane tells him he’ll have it by the next day. He then calls Emily, who thinks he’s checking out a villa in Tuscany. Sark mentions to him a job he has to do at a bank and says that he thinks it’s too dangerous for Sloane to do, since he’s probably wanted. Sloane has been working on this for 30 years and refuses to let anyone else “take the final steps.” At the ops center, Jack tells everyone that Sloane seems to be in Switzerland. Vaughn notes that he knows a headhunter in Switzerland and may be able to get some information out of him.

In Switzerland, Sloane works with a man who provides prosthetics. Sydney and Vaughn meet with Vaughn’s contact and interrogate him into revealing that Sloane did hire some men. He also tells them that Elsa and Aaron are nearby. Sydney and Vaughn rescue them, then grab a guard’s cell phone to see if they can trace any calls back to Sloane or Sark. At the CIA, Marshall explains to some agents how he was able to foil some of their plans when he was still with SD-6. Sydney calls him to find out who the guard called; Marshall sends her to a bank. Along the way, Vaughn calls the authorities to tell them there’s a robbery in process. A disguised Sloane and some men go to the bank to access a vault. Their money is actually rigged with explosives. After some destructive driving, Sydney gets herself and Vaughn to the bank. Sloane opens a briefcase in the vault and takes out the device Caplan was working on. Sydney tells the head of the bank to close down the vault. The man doesn’t think anything is awry because the security feed has been looped. Sydney catches Sloane and his guards on their way out and they all face off. He tells her that the building is rigged with C-4, so if they’re not allowed to walk out, no one will. He gets Sydney and Vaughn to lower their guns, then tells Sydney that she’ll be driving him out of there.